Results are presented for direct numerical simulations of hypersonic flow over an isolated roughness element located on a flat plate. The simulations were performed on a Cartesian grid with the roughness geometry imposed by a third-order cut-cell method. The simulations also utilize a fifth-order WENO scheme to capture any steep gradients in the flow created by the roughness. The combination results in a globally fourth-order scheme. Two-dimensional and three-dimensional test cases show very good agreement with results obtained from a body-fitted grid simulation. Preliminary results for Mach 6 flow over a k/δ = 0.75 cylindrical roughness are reported. In addition, results from a series of simulations of Mach 6 flow over a three-dimensional Gaussian roughness performed with a body-fitted grid are presented.